In my test vault I’ve got one file called Log. All of the following will link to that file:
[[Log]], [[log]], [[lOg]], [[LOG]]
I’ve also got two files called another and Another. They can be a little more finicky, but when I use [[ano it shows the file path in the auto completion list, so I can choose the “correct” one. If I don’t select one with a path, it’s kind of random which one it chooses.
So I’m not sure if that answers any of your concerns, but I’m using the autocompletion to select the “correct” version when I’ve got duplicated files in my vault. I’ve not experienced any issues so far, with referencing files, but your mileage may vary.